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Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble

As the biomedical impact of small RNAs grows, so does the need to understand competing structural alternatives for regions of functional interest. Suboptimal structure analysis provides significantly more RNA base pairing information than a single minimum free energy prediction. Yet computational en...

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Detalles Bibliográficos
Autores principales: Rogers, Emily, Heitsch, Christine E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267672/
https://www.ncbi.nlm.nih.gov/pubmed/25392423
http://dx.doi.org/10.1093/nar/gku959
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author Rogers, Emily
Heitsch, Christine E.
author_facet Rogers, Emily
Heitsch, Christine E.
author_sort Rogers, Emily
collection PubMed
description As the biomedical impact of small RNAs grows, so does the need to understand competing structural alternatives for regions of functional interest. Suboptimal structure analysis provides significantly more RNA base pairing information than a single minimum free energy prediction. Yet computational enhancements like Boltzmann sampling have not been fully adopted by experimentalists since identifying meaningful patterns in this data can be challenging. Profiling is a novel approach to mining RNA suboptimal structure data which makes the power of ensemble-based analysis accessible in a stable and reliable way. Balancing abstraction and specificity, profiling identifies significant combinations of base pairs which dominate low-energy RNA secondary structures. By design, critical similarities and differences are highlighted, yielding crucial information for molecular biologists. The code is freely available via http://gtfold.sourceforge.net/profiling.html.
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spelling pubmed-42676722014-12-23 Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble Rogers, Emily Heitsch, Christine E. Nucleic Acids Res Methods Online As the biomedical impact of small RNAs grows, so does the need to understand competing structural alternatives for regions of functional interest. Suboptimal structure analysis provides significantly more RNA base pairing information than a single minimum free energy prediction. Yet computational enhancements like Boltzmann sampling have not been fully adopted by experimentalists since identifying meaningful patterns in this data can be challenging. Profiling is a novel approach to mining RNA suboptimal structure data which makes the power of ensemble-based analysis accessible in a stable and reliable way. Balancing abstraction and specificity, profiling identifies significant combinations of base pairs which dominate low-energy RNA secondary structures. By design, critical similarities and differences are highlighted, yielding crucial information for molecular biologists. The code is freely available via http://gtfold.sourceforge.net/profiling.html. Oxford University Press 2014-12-16 2014-11-11 /pmc/articles/PMC4267672/ /pubmed/25392423 http://dx.doi.org/10.1093/nar/gku959 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Methods Online
Rogers, Emily
Heitsch, Christine E.
Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble
title Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble
title_full Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble
title_fullStr Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble
title_full_unstemmed Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble
title_short Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble
title_sort profiling small rna reveals multimodal substructural signals in a boltzmann ensemble
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267672/
https://www.ncbi.nlm.nih.gov/pubmed/25392423
http://dx.doi.org/10.1093/nar/gku959
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